1
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Hartley A, Burger L, Wincek CL, Dons L, Li T, Grewenig A, Taşgın T, Urban M, Roig-Merino A, Ghazvini M, Harbottle RP. A Simple Nonviral Method to Generate Human Induced Pluripotent Stem Cells Using SMAR DNA Vectors. Genes (Basel) 2024; 15:575. [PMID: 38790204 PMCID: PMC11121542 DOI: 10.3390/genes15050575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are a powerful tool for biomedical research, but their production presents challenges and safety concerns. Yamanaka and Takahashi revolutionised the field by demonstrating that somatic cells could be reprogrammed into pluripotent cells by overexpressing four key factors for a sufficient time. iPSCs are typically generated using viruses or virus-based methods, which have drawbacks such as vector persistence, risk of insertional mutagenesis, and oncogenesis. The application of less harmful nonviral vectors is limited as conventional plasmids cannot deliver the levels or duration of the factors necessary from a single transfection. Hence, plasmids that are most often used for reprogramming employ the potentially oncogenic Epstein-Barr nuclear antigen 1 (EBNA-1) system to ensure adequate levels and persistence of expression. In this study, we explored the use of nonviral SMAR DNA vectors to reprogram human fibroblasts into iPSCs. We show for the first time that iPSCs can be generated using nonviral plasmids without the use of EBNA-1 and that these DNA vectors can provide sufficient expression to induce pluripotency. We describe an optimised reprogramming protocol using these vectors that can produce high-quality iPSCs with comparable pluripotency and cellular function to those generated with viruses or EBNA-1 vectors.
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Affiliation(s)
- Anna Hartley
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Luisa Burger
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Cornelia L. Wincek
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
| | - Lieke Dons
- Erasmus MC iPS Core Facility, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands (M.G.)
| | - Tracy Li
- Erasmus MC iPS Core Facility, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands (M.G.)
| | - Annabel Grewenig
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
| | - Toros Taşgın
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Manuela Urban
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Alicia Roig-Merino
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Mehrnaz Ghazvini
- Erasmus MC iPS Core Facility, Erasmus Medical Centre, 3015 GD Rotterdam, The Netherlands (M.G.)
| | - Richard P. Harbottle
- DNA Vector Laboratory, German Cancer Research Center, 69120 Heidelberg, Germany; (A.H.); (A.G.); (A.R.-M.)
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2
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Khan SU, Khan MU, Khan MI, Kalsoom F, Zahra A. Current Landscape and Emerging Opportunities of Gene Therapy with Non-viral Episomal Vectors. Curr Gene Ther 2023; 23:135-147. [PMID: 36200188 DOI: 10.2174/1566523222666221004100858] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 11/22/2022]
Abstract
Gene therapy has proven to be extremely beneficial in the management of a wide range of genetic disorders for which there are currently no or few effective treatments. Gene transfer vectors are very significant in the field of gene therapy. It is possible to attach a non-viral attachment vector to the donor cell chromosome instead of integrating it, eliminating the negative consequences of both viral and integrated vectors. It is a safe and optimal express vector for gene therapy because it does not cause any adverse effects. However, the modest cloning rate, low expression, and low clone number make it unsuitable for use in gene therapy. Since the first generation of non-viral attachment episomal vectors was constructed, various steps have been taken to regulate their expression and stability, such as truncating the MAR element, lowering the amount of CpG motifs, choosing appropriate promoters and utilizing regulatory elements. This increases the transfection effectiveness of the non-viral attachment vector while also causing it to express at a high level and maintain a high level of stability. A vector is a genetic construct commonly employed in gene therapy to treat various systemic disorders. This article examines the progress made in the development of various optimization tactics for nonviral attachment vectors and the future applications of these vectors in gene therapy.
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Affiliation(s)
- Safir Ullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Munir Ullah Khan
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, International Research Center for X Polymers, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027 China
| | - Muhammad Imran Khan
- School of Life Sciences and Medicine, University of Science and Technology of China,Hefei 230027,People's Republic of China
- Department of Pathology, District Headquarters Hospital Jhang 35200, Punjab Province, Islamic Republic of Pakistan
| | - Fadia Kalsoom
- Department of Pathology, District Headquarters Hospital Jhang 35200, Punjab Province, Islamic Republic of Pakistan
| | - Aqeela Zahra
- Department of Family and Community Medicine. College of Medicine, University of Ha'il, Ha'il 81451, Saudi Arabia
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3
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Episomes and Transposases-Utilities to Maintain Transgene Expression from Nonviral Vectors. Genes (Basel) 2022; 13:genes13101872. [PMID: 36292757 PMCID: PMC9601623 DOI: 10.3390/genes13101872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
The efficient delivery and stable transgene expression are critical for applications in gene therapy. While carefully selected and engineered viral vectors allowed for remarkable clinical successes, they still bear significant safety risks. Thus, nonviral vectors are a sound alternative and avoid genotoxicity and adverse immunological reactions. Nonviral vector systems have been extensively studied and refined during the last decades. Emerging knowledge of the epigenetic regulation of replication and spatial chromatin organisation, as well as new technologies, such as Crispr/Cas, were employed to enhance the performance of different nonviral vector systems. Thus, nonviral vectors are in focus and hold some promising perspectives for future applications in gene therapy. This review addresses three prominent nonviral vector systems: the Sleeping Beauty transposase, S/MAR-based episomes, and viral plasmid replicon-based EBV vectors. Exemplarily, we review different utilities, modifications, and new concepts that were pursued to overcome limitations regarding stable transgene expression and mitotic stability. New insights into the nuclear localisation of nonviral vector molecules and the potential consequences thereof are highlighted. Finally, we discuss the remaining limitations and provide an outlook on possible future developments in nonviral vector technology.
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4
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Roig-Merino A, Urban M, Bozza M, Peterson JD, Bullen L, Büchler-Schäff M, Stäble S, van der Hoeven F, Müller-Decker K, McKay TR, Milsom MD, Harbottle RP. An episomal DNA vector platform for the persistent genetic modification of pluripotent stem cells and their differentiated progeny. Stem Cell Reports 2021; 17:143-158. [PMID: 34942088 PMCID: PMC8758943 DOI: 10.1016/j.stemcr.2021.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/14/2022] Open
Abstract
The genetic modification of stem cells (SCs) is typically achieved using integrating vectors, whose potential integrative genotoxicity and propensity for epigenetic silencing during differentiation limit their application. The genetic modification of cells should provide sustainable levels of transgene expression, without compromising the viability of a cell or its progeny. We developed nonviral, nonintegrating, and autonomously replicating minimally sized DNA nanovectors to persistently genetically modify SCs and their differentiated progeny without causing any molecular or genetic damage. These DNA vectors are capable of efficiently modifying murine and human pluripotent SCs with minimal impact and without differentiation-mediated transgene silencing or vector loss. We demonstrate that these vectors remain episomal and provide robust and sustained transgene expression during self-renewal and targeted differentiation of SCs both in vitro and in vivo through embryogenesis and differentiation into adult tissues, without damaging their phenotypic characteristics. Nanovectors are used to engineer SCs efficiently, safely, and persistently Isogenic SC lines retain their capacity for self-renewal and pluripotency Nanovectors survive reprogramming and differentiation without loss or silencing Nanovectors are a universal genetic tool for the modification of any cell
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Affiliation(s)
- Alicia Roig-Merino
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Manuela Urban
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Matthias Bozza
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Julia D Peterson
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Louise Bullen
- Stem Cell Biology, Manchester Metropolitan University (MMU), Manchester M1 5GD, UK
| | - Marleen Büchler-Schäff
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (Hi-STEM), Heidelberg 69120, Germany; Division of Experimental Hematology, DKFZ, Heidelberg 69120, Germany
| | - Sina Stäble
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (Hi-STEM), Heidelberg 69120, Germany; Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, Heidelberg 69120, Germany
| | | | | | - Tristan R McKay
- Stem Cell Biology, Manchester Metropolitan University (MMU), Manchester M1 5GD, UK
| | - Michael D Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (Hi-STEM), Heidelberg 69120, Germany; Division of Experimental Hematology, DKFZ, Heidelberg 69120, Germany
| | - Richard P Harbottle
- DNA Vectors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
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5
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Mulia GE, Picanço-Castro V, Stavrou EF, Athanassiadou A, Figueiredo ML. Advances in the Development and the Applications of Non-viral, Episomal Vectors for Gene Therapy. Hum Gene Ther 2021; 32:1076-1095. [PMID: 34348480 PMCID: PMC8819515 DOI: 10.1089/hum.2020.310] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Nonviral and nonintegrating episomal vectors are reemerging as a valid, alternative technology to integrating viral vectors for gene therapy, due to their more favorable safety profile, significantly lower risk for insertional mutagenesis, and a lesser potential for innate immune reactions, in addition to their low production cost. Over the past few years, attempts have been made to generate highly functional nonviral vectors that display long-term maintenance within cells and promote more sustained gene expression relative to conventional plasmids. Extensive research into the parameters that stabilize the episomal DNA within dividing and nondividing cells has shed light into the genetic and epigenetic mechanisms that govern replication and transcription of episomal DNA within a mammalian nucleus in long-term cell culture. Episomal vectors based on scaffold/matrix attachment regions (S/MARs) do not integrate into the genomic DNA and address the serious problem of plasmid loss during mitosis by providing mitotic stability to established plasmids, which results in long-term transfection and transgene expression. The inclusion, in such vectors, of an origin of replication—initiation region—from the human genome has greatly enhanced their performance in primary cell culture. A number of vectors that function as episomes have arisen, which are either devoid or depleted of harmful CpG sequences and bacterial genes, and their effectiveness, as well as that of nonintegrating viral episomes, is enhanced when combined with S/MAR elements. As a result of these advances, an “S/MAR technology” has emerged for the production of efficient episomal vectors. Significant research continues in this field and innovations, in combination with promising systems based on nanoparticles and potentially combined with physical delivery methods, will enable the generation of optimized systems with scale-up and clinical application suitability utilizing episomal vectors.
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Affiliation(s)
- Grace E Mulia
- Purdue University, Basic Medical Sciences, West Lafayette, Indiana, United States;
| | - Virginia Picanço-Castro
- University of Sao Paulo Faculty of Medicine of Ribeirao Preto, 54539, Center for Cell-based Therapy, Ribeirao Preto, São Paulo, Brazil;
| | - Eleana F Stavrou
- University of Patras, Department of General Biology, Patras, Greece;
| | - Aglaia- Athanassiadou
- University of Patras Medical School, General Biology, Asklepiou str, University Campus, Rion Patras, Greece, 26504;
| | - Marxa L Figueiredo
- Purdue University, Basic Medical Sciences, 625 Harrison St., LYNN 2177, West Lafayette, Indiana, United States, 47907;
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6
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Regulation of HPV18 Genome Replication, Establishment and Persistence by Sequences in the Viral Upstream Regulatory Region. J Virol 2021; 95:e0068621. [PMID: 34232709 DOI: 10.1128/jvi.00686-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During persistent human papillomavirus infection, the viral genome replicates as an extrachromosomal plasmid that is efficiently partitioned to daughter cells during cell division. We have previously shown that an element which overlaps the HPV18 transcriptional enhancer promotes stable DNA replication of replicons containing the viral replication origin. Here we perform comprehensive analyses to elucidate the function of this maintenance element. We conclude that no unique element or binding site in this region is absolutely required for persistent replication and partitioning, and instead propose that the overall chromatin architecture of this region is important to promote efficient use of the replication origin. These results have important implications on the genome partitioning mechanism of papillomaviruses. Importance Persistent infection with oncogenic HPVs is responsible for ∼5% human cancers. The viral DNA replicates as an extrachromosomal plasmid and is partitioned to daughter cells in dividing keratinocytes. Using a complementation assay that allows us to separate viral transcription and replication, we provide insight into viral sequences that are required for long term replication and persistence in keratinocytes. Understanding how viral genomes replicate persistently for such long periods of time will guide the development of anti-viral therapies.
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7
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Bozza M, Green EW, Espinet E, De Roia A, Klein C, Vogel V, Offringa R, Williams JA, Sprick M, Harbottle RP. Novel Non-integrating DNA Nano-S/MAR Vectors Restore Gene Function in Isogenic Patient-Derived Pancreatic Tumor Models. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:957-968. [PMID: 32420409 PMCID: PMC7218229 DOI: 10.1016/j.omtm.2020.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022]
Abstract
We describe herein non-integrating minimally sized nano-S/MAR DNA vectors, which can be used to genetically modify dividing cells in place of integrating vectors. They represent a unique genetic tool, which avoids vector-mediated damage. Previous work has shown that DNA vectors comprising a mammalian S/MAR element can provide persistent mitotic stability over hundreds of cell divisions, resisting epigenetic silencing and thereby allowing sustained transgene expression. The composition of the original S/MAR vectors does present some inherent limitations that can provoke cellular toxicity. Herein, we present a new system, the nano-S/MAR, which drives higher transgene expression and has improved efficiency of establishment, due to the minimal impact on cellular processes and perturbation of the endogenous transcriptome. We show that these features enable the hitherto challenging genetic modification of patient-derived cells to stably restore the tumor suppressor gene SMAD4 to a patient-derived SMAD4 knockout pancreatic cancer line. Nano-S/MAR modification does not alter the molecular or phenotypic integrity of the patient-derived cells in cell culture and xenograft mouse models. In conclusion, we show that these DNA vectors can be used to persistently modify a range of cells, providing sustained transgene expression while avoiding the risks of insertional mutagenesis and other vector-mediated toxicity.
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Affiliation(s)
- Matthias Bozza
- DNA Vector Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
| | - Edward W Green
- Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Elisa Espinet
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Alice De Roia
- DNA Vector Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
| | - Corinna Klein
- Stem Cells and Metastasis, Hi-Stem Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Vanessa Vogel
- Stem Cells and Metastasis, Hi-Stem Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Rienk Offringa
- Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | | | - Martin Sprick
- Stem Cells and Metastasis, Hi-Stem Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Richard P Harbottle
- DNA Vector Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
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8
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Xu ZJ, Jia YL, Wang M, Yi DD, Zhang WL, Wang XY, Zhang JH. Effect of promoter, promoter mutation and enhancer on transgene expression mediated by episomal vectors in transfected HEK293, Chang liver and primary cells. Bioengineered 2020; 10:548-560. [PMID: 31668126 PMCID: PMC6844389 DOI: 10.1080/21655979.2019.1684863] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The episomal vector cannot integrate into the host cell chromosome, which has no potential risk in gene therapy. However, the low level of transgene expression driven by episomal vectors needs to be solved. In this study, we investigated the effects of enhancers, promoters and promoter variants on transgene expression levels driven by episomal vectors in HEK293, Chang liver and primary cells. Results showed that all eight cis-acting elements used could increase transfection efficiency and transient eGFP expression in transfected HEK293 and Chang liver cells. In stably transfected mammalian cells, the elongation factor-1 alpha (EF-1α) promoter and mutant-404 showed high and stable transgene expression. The mechanisms might be related to the type and quantity of transcription factor regulatory elements. Moreover, quantitative reverse transcription polymerase chain reaction analysis showed that mRNA expression levels were not directly proportional to protein expression levels. Furthermore, the EF-1α promoter conferred high transgene expression levels in primary cells, and the plasmid was also present in the episomal state. Taken together, these results provided valuable information for improving transgene expression with episomal vectors in mammalian cells.
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Affiliation(s)
- Zhong-Jie Xu
- Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yan-Long Jia
- Pharmacy collage, Xinxiang Medical University, Xinxiang, Henan, China
| | - Meng Wang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Dan-Dan Yi
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Wei-Li Zhang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiao-Yin Wang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jun-He Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
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9
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Wang XY, Zhang X, Wang TY, Jia YL, Xu DH, Yi DD. Shortened nuclear matrix attachment regions are sufficient for replication and maintenance of episomes in mammalian cells. Mol Biol Cell 2019; 30:2761-2770. [PMID: 31509492 PMCID: PMC6789156 DOI: 10.1091/mbc.e19-02-0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Matrix attachment regions (MARs) can mediate the replication of vector episomes in mammalian cells; however, the molecular mode of action remains unclear. Here, we assessed the characteristics of MARs and the mechanism that mediates episomal vector replication in mammalian cells. Five shortened subfragments of β-interferon MAR fragments were cloned and transferred into CHO cells, and transgene expression levels, presence of the gene, and the episomal maintenance mechanism were determined. Three shortened MAR derivatives (position 781–1320, 1201–1740, and 1621–2201) retained full MAR activity and mediated episomal vector replication. Moreover, the three shortened MARs showed higher transgene expression levels, greater efficiency in colony formation, and more persistent transgene expression compared with those of the original pEPI-1 plasmid, and three functional truncated MARs can bind to SAF-A MAR-binding protein. These results suggest that shortened MARs are sufficient for replication and maintenance of episomes in CHO cells.
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Affiliation(s)
- Xiao-Yin Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang 453003, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Xi Zhang
- International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang 453003, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Yan-Long Jia
- Pharmacy Collage, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Dan-Hua Xu
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang 453003, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Dan-Dan Yi
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang 453003, Henan, China.,International Joint Research Laboratory for Recombiant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang 453003, Henan, China
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10
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Efficient episomal gene transfer to human hepatic cells using the pFAR4–S/MAR vector. Mol Biol Rep 2019; 46:3203-3211. [DOI: 10.1007/s11033-019-04777-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/20/2019] [Indexed: 12/16/2022]
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11
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Wagner S, McCracken J, Bruszies S, Broadhurst R, Wells DN, Oback B, Bode J, Laible G. Episomal minicircles persist in periods of transcriptional inactivity and can be transmitted through somatic cell nuclear transfer into bovine embryos. Mol Biol Rep 2019; 46:1737-1746. [PMID: 30694456 DOI: 10.1007/s11033-019-04624-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/18/2019] [Indexed: 12/14/2022]
Abstract
Episomal plasmids based on a scaffold/matrix attachment region (S/MAR) are extrachromosomal DNA entities that replicate once per cell cycle and are stably maintained in cells or tissue. We generated minicircles, episomal plasmids devoid of bacterial sequences, and show that they are stably transmitted in clonal primary bovine fibroblasts without selection pressure over more than two months. Total DNA, plasmid extraction and fluorescence in situ hybridization (FISH) analyses suggest that the minicircles remained episomal and were not integrated into the genome. Minicircles survived extended periods in serum-starved cells, which indicates that ongoing transcription in non-proliferating cells is not necessary for the maintenance of S/MAR-episomes. To test whether minicircles endure the process of somatic cell nuclear transfer (SCNT), we used cell-cycle synchronized, serum-starved, minicircle-containing cells. Analysis of cells outgrown from SCNT-derived blastocysts shows that the minicircles are maintained through SCNT and early embryonic development, which raises the prospect of using cell lines with episomal minicircles for the generation of transgenic animals.
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Affiliation(s)
- Stefan Wagner
- AgResearch Limited, Ruakura Research Centre, Hamilton, 3240, New Zealand. .,Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
| | - Judi McCracken
- AgResearch Limited, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - Sabine Bruszies
- AgResearch Limited, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - Ric Broadhurst
- AgResearch Limited, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - David N Wells
- AgResearch Limited, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - Björn Oback
- AgResearch Limited, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - Jürgen Bode
- Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Götz Laible
- AgResearch Limited, Ruakura Research Centre, Hamilton, 3240, New Zealand
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12
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Hagedorn C, Gogol-Döring A, Schreiber S, Epplen JT, Lipps HJ. Genome-wide profiling of S/MAR-based replicon contact sites. Nucleic Acids Res 2017; 45:7841-7854. [PMID: 28609784 PMCID: PMC5570033 DOI: 10.1093/nar/gkx522] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 06/05/2017] [Indexed: 11/14/2022] Open
Abstract
Autonomously replicating vectors represent a simple and versatile model system for genetic modifications, but their localization in the nucleus and effect on endogenous gene expression is largely unknown. Using circular chromosome conformation capture we mapped genomic contact sites of S/MAR-based replicons in HeLa cells. The influence of cis-active sequences on genomic localization was assessed using replicons containing either an insulator sequence or an intron. While the original and the insulator-containing replicons displayed distinct contact sites, the intron-containing replicon showed a rather broad genomic contact pattern. Our results indicate a preference for certain chromatin structures and a rather non-dynamic behaviour during mitosis. Independent of inserted cis-active elements established vector molecules reside preferentially within actively transcribed regions, especially within promoter sequences and transcription start sites. However, transcriptome analyses revealed that established S/MAR-based replicons do not alter gene expression profiles of host genome. Knowledge of preferred contact sites of exogenous DNA, e.g. viral or non-viral episomes, contribute to our understanding of episome behaviour in the nucleus and can be used for vector improvement and guiding of DNA sequences to specific subnuclear sites.
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Affiliation(s)
- Claudia Hagedorn
- University of Witten/Herdecke, ZBAF, Institute of Cell Biology, Stockumer Strasse 10, 58453 Witten, Germany
| | - Andreas Gogol-Döring
- Technische Hochschule Mittelhessen (University of Applied Sciences), Department of Bioinformatics, Wiesenstrasse 14, 35390 Gießen, Germany
| | - Sabrina Schreiber
- Department of Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany
| | - Jörg T Epplen
- University of Witten/Herdecke, ZBAF, Institute of Cell Biology, Stockumer Strasse 10, 58453 Witten, Germany.,Department of Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany
| | - Hans J Lipps
- University of Witten/Herdecke, ZBAF, Institute of Cell Biology, Stockumer Strasse 10, 58453 Witten, Germany
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Hagedorn C, Schnödt-Fuchs M, Boehme P, Abdelrazik H, Lipps HJ, Büning H. S/MAR Element Facilitates Episomal Long-Term Persistence of Adeno-Associated Virus Vector Genomes in Proliferating Cells. Hum Gene Ther 2017; 28:1169-1179. [PMID: 28665147 DOI: 10.1089/hum.2017.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are one of the most frequently applied gene transfer systems in research and human clinical trials. Since AAV vectors do not possess an integrase activity, application is restricted to terminally differentiated tissues if transgene expression is required long term. To overcome this limitation and to generate AAV vectors that persist episomally in dividing cells, AAV vector genomes were equipped with a scaffold/matrix attachment region (S/MAR). After a mild antibiotic selection, cells transduced with AAV-S/MAR established colonies that maintained long-term transgene expression (>50 population doublings) from replicating AAV vector episomes in the absence of further selection. Unexpectedly, with a lesser but still significant efficiency, the control vector (AAV-ΔS/MAR), a standard single-stranded AAV vector, also established stable transgene-expressing colonies, most of which were maintained as replicating episomes rather than integrated vector genomes. Thus, based on the result in HeLa cells, it is concluded that AAV vector genomes per se possess the ability to establish episomal maintenance in proliferating cells, a feature that can be enhanced by incorporation of a foreign genomic element such as an S/MAR element.
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Affiliation(s)
- Claudia Hagedorn
- 1 Institute of Cell Biology, ZBAF, University of Witten/Herdecke , Witten, Germany
| | - Maria Schnödt-Fuchs
- 2 Laboratory for AAV Vector Development, Center for Molecular Medicine Cologne (CMMC), University of Cologne , Cologne, Germany .,3 Department I of Internal Medicine, University Hospital Cologne , Cologne, Germany .,4 German Center for Infection Research (DZIF) , partner sites Bonn-Cologne and Hannover-Braunschweig
| | - Philip Boehme
- 1 Institute of Cell Biology, ZBAF, University of Witten/Herdecke , Witten, Germany .,5 Institute of Virology and Microbiology, ZBAF, University of Witten/Herdecke , Witten, Germany
| | - Heba Abdelrazik
- 2 Laboratory for AAV Vector Development, Center for Molecular Medicine Cologne (CMMC), University of Cologne , Cologne, Germany .,6 Clinical Pathology Department, Faculty of Medicine, Cairo University , Cairo, Egypt
| | - Hans J Lipps
- 1 Institute of Cell Biology, ZBAF, University of Witten/Herdecke , Witten, Germany
| | - Hildegard Büning
- 2 Laboratory for AAV Vector Development, Center for Molecular Medicine Cologne (CMMC), University of Cologne , Cologne, Germany .,3 Department I of Internal Medicine, University Hospital Cologne , Cologne, Germany .,4 German Center for Infection Research (DZIF) , partner sites Bonn-Cologne and Hannover-Braunschweig.,7 Laboratory for Infection Biology and Gene Transfer, Institute of Experimental Hematology, Hannover Medical School , Hannover, Germany
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Wang X, Xu Z, Tian Z, Zhang X, Xu D, Li Q, Zhang J, Wang T. The EF-1α promoter maintains high-level transgene expression from episomal vectors in transfected CHO-K1 cells. J Cell Mol Med 2017; 21:3044-3054. [PMID: 28557288 PMCID: PMC5661254 DOI: 10.1111/jcmm.13216] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/01/2017] [Indexed: 02/03/2023] Open
Abstract
In our previous study, we demonstrated that episomal vectors based on the characteristic sequence of matrix attachment regions (MARs) and containing the cytomegalovirus (CMV) promoter allow transgenes to be maintained episomally in Chinese hamster ovary (CHO) cells. However, the transgene expression was unstable and the number of copies was low. In this study, we focused on enhancers, various promoters and promoter variants that could improve the transgene expression stability, expression magnitude (level) and the copy number of a MAR‐based episomal vector in CHO‐K1 cells. In comparison with the CMV promoter, the eukaryotic translation elongation factor 1 α (EF‐1α, gene symbol EEF1A1) promoter increased the transfection efficiency, the transgene expression, the proportion of expression‐positive clones and the copy number of the episomal vector in long‐term culture. By contrast, no significant positive effects were observed with an enhancer, CMV promoter variants or CAG promoter in the episomal vector in long‐term culture. Moreover, the high‐expression clones harbouring the EF‐1α promoter tended to be more stable in long‐term culture, even in the absence of selection pressure. According to these findings, we concluded that the EF‐1α promoter is a potent regulatory sequence for episomal vectors because it maintains high transgene expression, transgene stability and copy number. These results provide valuable information on improvement of transgene stability and the copy number of episomal vectors.
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Affiliation(s)
- Xiaoyin Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang, Henan, China
| | - Zhongjie Xu
- Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhengwei Tian
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xi Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Danhua Xu
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Qin Li
- Test Laboratory, Xinxiang Medical University, Xinxiang, Henan, China
| | - Junhe Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tianyun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
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Stavrou EF, Lazaris VM, Giannakopoulos A, Papapetrou E, Spyridonidis A, Zoumbos NC, Gkountis A, Athanassiadou A. The β-globin Replicator greatly enhances the potential of S/MAR based episomal vectors for gene transfer into human haematopoietic progenitor cells. Sci Rep 2017; 7:40673. [PMID: 28106085 PMCID: PMC5247744 DOI: 10.1038/srep40673] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/09/2016] [Indexed: 11/08/2022] Open
Abstract
Specific human chromosomal elements enhance the performance of episomal gene-transfer vectors. S/MAR-based episomal vector pEPI-eGFP transfects CD34+ haematopoietic cells, but only transiently. To address this issue we reinforced (1) transgene transcription by replacing the CMV promoter driving eGFP with the EF1/HTLV or SFFV promoters to produce vectors pEPI-EF1/HTLV and pEPI-SFFV, respectively; and (2) plasmid replication by inserting the replication-Initiation Region (IR) from the β-globin locus into vector pEPI-SFFV to produce vector pEP-IR. All vectors supported stable transfections in K562 cells. Transfections of CD34+ cells from peripheral blood of healthy donors reached 30% efficiency. Upon evaluation of CD34+/eGFP+ cells in colony-forming cell (CFC) assays, vector pEP-IR showed superior performance after 14 days, by fluorescent microscopy: 100% eGFP+-colonies against 0% for pEPI-eGFP, 56.9% for pEPI-SFFV and 49.8% for pEPI-EF1/HTLV; 50% more plasmid copies per cell and 3-fold eGFP expression compared to the latter two constructs, by quantitative (q)PCR and RT-qPCR, respectively. Importantly, the establishment rate in CFC assays was 15% for pEP-IR against 5.5% for pEPI-SFFV and 5% for pEPI-EF1/HTLV. Vector pEP-IR shows extremely low delivery rate but supports eGFP expression in thalassaemic mouse haematopoietic progenitor cells. The IR is a novel human control element for improved episomal gene transfer into progenitor cells.
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Affiliation(s)
- Eleana F. Stavrou
- Department of General Biology, School of Medicine, University of Patras, Greece
| | | | | | - Eirini Papapetrou
- Department of General Biology, School of Medicine, University of Patras, Greece
| | - Alexandros Spyridonidis
- Haematology Unit Department of Internal Medicine, School of Medicine, University of Patras, Greece
| | - Nikolas C. Zoumbos
- Haematology Unit Department of Internal Medicine, School of Medicine, University of Patras, Greece
| | - Antonis Gkountis
- Gene and Cell Therapy Center, Haematology Department-BMT Unit, George Papanicolaou Hospital, Thessaloniki, Greece
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16
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Impact of Different Promoters on Episomal Vectors Harbouring Characteristic Motifs of Matrix Attachment Regions. Sci Rep 2016; 6:26446. [PMID: 27226236 PMCID: PMC4881036 DOI: 10.1038/srep26446] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/29/2016] [Indexed: 12/19/2022] Open
Abstract
We previously demonstrated that the characteristic sequence of matrix attachment regions (MARs) allows transgenes to be maintained episomally in CHO cells. In the present study, six commonly used promoters from human cytomegalovirus major immediate-early (CMV), simian vacuolating virus 40 (SV40), Rous sarcoma virus, Homo sapiens ubiquitin C, phosphoglycerate kinase, and β-globin, respectively, were evaluated to determine their effects on transgene expression and stability in CHO cells stably transfected via the episomal vector harbouring characteristic MAR motifs. The CHO cells were transfected with vectors and then screened using G418, after which the stably transfected cells were split into two and further cultured either in the presence or absence of G418. Of the six promoters, the CMV promoter yielded the highest transgene expression levels and the highest transfection efficiency, whereas the SV40 promoter maintained transgene expression more stably during long-term culture than the other promoters did. The CMV and SV40 promoter-containing vectors were furthermore episomally maintained and conferred sustained eGFP expression in the cells even under nonselective conditions. On the basis of these findings, we conclude that the CMV promoter performs best in terms of yielding both high expression levels and high levels of stability using this episomal vector system.
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Hagedorn C, Lipps HJ, Rupprecht S. The epigenetic regulation of autonomous replicons. Biomol Concepts 2015; 1:17-30. [PMID: 25961982 DOI: 10.1515/bmc.2010.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The discovery of autonomous replicating sequences (ARSs) in Saccharomyces cerevisiae in 1979 was considered a milestone in unraveling the regulation of replication in eukaryotic cells. However, shortly afterwards it became obvious that in Saccharomyces pombe and all other higher organisms ARSs were not sufficient to initiate independent replication. Understanding the mechanisms of replication is a major challenge in modern cell biology and is also a prerequisite to developing application-oriented autonomous replicons for gene therapeutic treatments. This review will focus on the development of non-viral episomal vectors, their use in gene therapeutic applications and our current knowledge about their epigenetic regulation.
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Lin Y, Li Z, Wang T, Wang X, Wang L, Dong W, Jing C, Yang X. MAR characteristic motifs mediate episomal vector in CHO cells. Gene 2015; 559:137-43. [DOI: 10.1016/j.gene.2015.01.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/05/2015] [Accepted: 01/13/2015] [Indexed: 01/24/2023]
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Han Z, Banworth MJ, Makkia R, Conley SM, Al-Ubaidi MR, Cooper MJ, Naash MI. Genomic DNA nanoparticles rescue rhodopsin-associated retinitis pigmentosa phenotype. FASEB J 2015; 29:2535-44. [PMID: 25713057 DOI: 10.1096/fj.15-270363] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/09/2015] [Indexed: 01/10/2023]
Abstract
Mutations in the rhodopsin gene cause retinal degeneration and clinical phenotypes including retinitis pigmentosa (RP) and congenital stationary night blindness. Effective gene therapies have been difficult to develop, however, because generating precise levels of rhodopsin expression is critical; overexpression causes toxicity, and underexpression would result in incomplete rescue. Current gene delivery strategies routinely use cDNA-based vectors for gene targeting; however, inclusion of noncoding components of genomic DNA (gDNA) such as introns may help promote more endogenous regulation of gene expression. Here we test the hypothesis that inclusion of genomic sequences from the rhodopsin gene can improve the efficacy of rhodopsin gene therapy in the rhodopsin knockout (RKO) mouse model of RP. We utilize our compacted DNA nanoparticles (NPs), which have the ability to transfer larger and more complex genetic constructs, to deliver murine rhodopsin cDNA or gDNA. We show functional and structural improvements in RKO eyes for up to 8 months after NP-mediated gDNA but not cDNA delivery. Importantly, in addition to improvements in rod function, we observe significant preservation of cone function at time points when cones in the RKO model are degenerated. These results suggest that inclusion of native expression elements, such as introns, can significantly enhance gene expression and therapeutic efficacy and may become an essential option in the array of available gene delivery tools.
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Affiliation(s)
- Zongchao Han
- *Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and Copernicus Therapeutics, Incorporated, Cleveland, Ohio, USA
| | - Marcellus J Banworth
- *Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and Copernicus Therapeutics, Incorporated, Cleveland, Ohio, USA
| | - Rasha Makkia
- *Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and Copernicus Therapeutics, Incorporated, Cleveland, Ohio, USA
| | - Shannon M Conley
- *Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and Copernicus Therapeutics, Incorporated, Cleveland, Ohio, USA
| | - Muayyad R Al-Ubaidi
- *Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and Copernicus Therapeutics, Incorporated, Cleveland, Ohio, USA
| | - Mark J Cooper
- *Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and Copernicus Therapeutics, Incorporated, Cleveland, Ohio, USA
| | - Muna I Naash
- *Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA; and Copernicus Therapeutics, Incorporated, Cleveland, Ohio, USA
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20
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Koirala A, Conley SM, Makkia R, Liu Z, Cooper MJ, Sparrow JR, Naash MI. Persistence of non-viral vector mediated RPE65 expression: case for viability as a gene transfer therapy for RPE-based diseases. J Control Release 2013; 172:745-52. [PMID: 24035979 DOI: 10.1016/j.jconrel.2013.08.299] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/22/2013] [Indexed: 11/25/2022]
Abstract
Mutations in the retinal pigment epithelium (RPE) gene RPE65 are associated with multiple blinding diseases including Leber's Congenital Amaurosis (LCA). Our goal has been to develop persistent, effective non-viral genetic therapies to treat this condition. Using precisely engineered DNA vectors and high capacity compacted DNA nanoparticles (NP), we previously demonstrated that both plasmid and NP forms of VMD2-hRPE65-S/MAR improved the disease phenotypes in an rpe65(-/-) model of LCA up to 6 months post-injection (PI), however the duration of this treatment efficacy was not established. Here, we test the ability of these vectors to sustain gene expression and phenotypic improvement for the life of the animal. NPs or naked DNA were subretinally injected in rpe65(-/-) mice at postnatal day (P) 16 and evaluated at 15 months PI. Quantitative real-time PCR (qRT-PCR) and immunofluorescence were performed at PI-15 months and demonstrated appreciable expression of transferred RPE65 (levels were 32% of wild-type [WT] for NPs and 44% of WT for naked DNA). No reduction in expression at the message level was observed from PI-6 month data. Spectral electroretinography (ERG) demonstrated significant improvement in cone ERG amplitudes in treated versus uninjected animals. Most importantly, we also observed reduced fundus autofluorescence in the eyes injected with NP and naked DNA compared to uninjected counterparts. Consistent with these observations, biochemical studies showed a reduction in the accumulation of toxic retinyl esters in treated mice, suggesting that the transferred hRPE65 was functional. These critical results indicate that both NP and uncompacted plasmid VMD2-hRPE65-S/MAR can mediate persistent, long-term improvement in an RPE-associated disease phenotype, and suggest that DNA NPs, which are non-toxic and have a large payload capacity, expand the treatment repertoire available for ocular gene therapy.
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Affiliation(s)
- Adarsha Koirala
- Department of Cell Biology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, BMSB 781, Oklahoma City, OK 73104, USA
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Genomic cis-acting Sequences Improve Expression and Establishment of a Nonviral Vector. MOLECULAR THERAPY. NUCLEIC ACIDS 2013; 2:e118. [PMID: 24002728 PMCID: PMC3759742 DOI: 10.1038/mtna.2013.47] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/21/2013] [Indexed: 01/30/2023]
Abstract
The vector pEPI was the first nonviral and episomally replicating vector. Its functional element is an expression unit linked to a chromosomal scaffold/matrix attached region (S/MAR). The vector replicates autonomously with low copy number in various cell lines, is mitotically stable in the absence of selection over hundreds of generations, and was successfully used for the efficient generation of genetically modified pigs. Since it is assumed that establishment of the vector is a stochastic event and strongly depends on the nuclear compartment it reaches after transfection, it is of great interest to identify genomic sequences that guide DNA sequences into certain nuclear compartments. Here we inserted genomic cis-acting sequences into pEPI and examined their impact on transgene expression, long-term stability, and vector establishment. We demonstrated that a ubiquitous chromatin-opening element (UCOE) mediated enhanced transgene expression, while an insulator sequence (cHS4) increased establishment efficiency, presumably via an additional interaction with the nuclear matrix. Thus, besides being a promising alternative to currently used viral vectors in gene therapeutic approaches, pEPI may also serve as a tool to study nuclear compartmentalization; identification of genomic cis-acting sequences that are involved in nuclear organization will contribute to our understanding of the interplay between transgene expression, plasmid establishment, and nuclear architecture.
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Development and validation of non-integrative, self-limited, and replicating minicircles for safe reporter gene imaging of cell-based therapies. PLoS One 2013; 8:e73138. [PMID: 24015294 PMCID: PMC3756008 DOI: 10.1371/journal.pone.0073138] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 07/24/2013] [Indexed: 12/24/2022] Open
Abstract
Reporter gene (RG) imaging of cell-based therapies provides a direct readout of therapeutic efficacy by assessing the fate of implanted cells. To permit long-term cellular imaging, RGs are traditionally required to be integrated into the cellular genome. This poses a potential safety risk and regulatory bottleneck for clinical translation as integration can lead to cellular transformation. To address this issue, we have developed non-integrative, replicating minicircles (MCs) as an alternative platform for safer monitoring of cells in living subjects. We developed both plasmids and minicircles containing the scaffold/matrix attachment regions (S/MAR) of the human interferon-beta gene, driven by the CMV promoter, and expressing the bioluminescence RG firefly luciferase. Constructs were transfected into breast cancer cells, and expanded S/MAR minicircle clones showed luciferase signal for greater than 3 months in culture and minicircles remained as episomes. Importantly, luciferase activity in clonal populations was slowly lost over time and this corresponded to a loss of episome, providing a way to reversibly label cells. To monitor cell proliferation in vivo, 1.5×106 cells carrying the S/MAR minicircle were implanted subcutaneously into mice (n = 5) and as tumors developed significantly more bioluminescence signal was noted at day 35 and 43 compared to day 7 post-implant (p<0.05). To our knowledge, this is the first work examining the use of episomal, self-limited, replicating minicircles to track the proliferation of cells using non-invasive imaging in living subjects. Continued development of S/MAR minicircles will provide a broadly applicable vector platform amenable with any of the numerous RG technologies available to allow therapeutic cell fate to be assessed in individual patients, and to achieve this without the need to manipulate the cell's genome so that safety concerns are minimized. This will lead to safe tools to assess treatment response at earlier time points and improve the precision of cell-based therapies.
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Modified S/MAR episomal vectors for stably expressing fluorescent protein-tagged transgenes with small cell-to-cell fluctuations. Anal Biochem 2013; 443:113-6. [PMID: 23969013 DOI: 10.1016/j.ab.2013.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/10/2013] [Indexed: 11/22/2022]
Abstract
We modified and tested scaffold/matrix attachment region (S/MAR) episomal vectors. The new vectors would be useful in obtaining cells stably expressing fluorescent protein-tagged transgenes with small, mostly within 10-fold cell-to-cell fluctuations. In the vectors, the same transcript directs episomal replication and expression of transgene/antibiotic marker, and only antibiotic selection without any other extra steps was sufficient to obtain desired stable cells, including those expressing two different proteins simultaneously. Furthermore, the two test cases (expression of human growth hormone in AtT20 and four protein kinase C isoforms in HEK293) would prove to be useful in visualizing and analyzing regulatory processes involving these proteins.
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Koirala A, Conley SM, Naash MI. A review of therapeutic prospects of non-viral gene therapy in the retinal pigment epithelium. Biomaterials 2013; 34:7158-67. [PMID: 23796578 DOI: 10.1016/j.biomaterials.2013.06.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 06/02/2013] [Indexed: 10/26/2022]
Abstract
Ocular gene therapy has been extensively explored in recent years as a therapeutic avenue to target diseases of the cornea, retina and retinal pigment epithelium (RPE). Adeno-associated virus (AAV)-mediated gene therapy has shown promise in several RPE clinical trials but AAVs have limited payload capacity and potential immunogenicity. Traditionally however, non-viral alternatives have been plagued by low transfection efficiency, short-term expression and low expression levels. Recently, these drawbacks have begun to be overcome by the use of specialty carriers such as polylysine, liposomes, or polyethyleneimines, and by inclusion of suitable DNA elements to enhance gene expression and longevity. Recent advancements in the field have yielded non-viral vectors that have favorable safety profiles, lack immunogenicity, exhibit long-term elevated gene expression, and show efficient transfection in the retina and RPE, making them poised to transition to clinical applications. Here we discuss the advancements in nanotechnology and vector engineering that have improved the prospects for clinical application of non-viral gene therapy in the RPE.
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Affiliation(s)
- Adarsha Koirala
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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25
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Haase R, Magnusson T, Su B, Kopp F, Wagner E, Lipps H, Baiker A, Ogris M. Generation of a tumor- and tissue-specific episomal non-viral vector system. BMC Biotechnol 2013; 13:49. [PMID: 23734827 PMCID: PMC3728224 DOI: 10.1186/1472-6750-13-49] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 05/28/2013] [Indexed: 02/08/2023] Open
Abstract
Background A key issue for safe and reproducible gene therapy approaches is the autologous and tissue-specific expression of transgenes. Tissue-specific expression in vivo is either achieved by transfer vectors that deliver the gene of interest into a distinct cell type or by use of tissue-specific expression cassettes. Here we present the generation of non-viral, episomally replicating vectors that are able to replicate in a tissue specific manner thus allowing tissue specific transgene expression in combination with episomal replication. The episomal replication of the prototype vector pEPI-1 and its derivatives depends exclusively on a transcription unit starting from a constitutively active promoter extending into the scaffold/matrix attachment region (S/MAR). Results Here, we exchanged the constitutive promoter in the pEPI derivative pEPito by the tumor specific alpha fetoprotein (AFP) or the muscle specific smooth muscle 22 (SM22) promoter leading to specific transgene expression in AFP positive human hepatocellular carcinoma (HUH7) and in a SM22 positive cell line, respectively. The incorporation of the hCMV enhancer element into the expression cassette further boosted the expression levels with both promoters. Tissue specific-replication could be exemplary proven for the smooth muscle protein 22 (SM22) promoter in vitro. With the AFP promoter-driven pEPito vector hepatocellular carcinoma-specific expression could be achieved in vivo after systemic vector application together with polyethylenimine as transfection enhancer. Conclusions In this study we present an episomal plasmid system designed for tissue specific transgene expression and replication. The human AFP-promoter in combination with the hCMV enhancer element was demonstrated to be a valuable tissue-specific promoter for targeting hepatocellular carcinomas with non-viral gene delivery system, and tissue specific replication could be shown in vitro with the muscle specific SM22 promoter. In combination with appropriate delivery systems, the tissue specific pEPito vector system will allow higher tissue-specificity with less undesired side effects and is suitable for long term transgene expression in vivo within gene therapeutical approaches.
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Affiliation(s)
- Rudolf Haase
- Department of Pharmacy, Center for Drug Research, Pharmaceutical Biotechnology, Ludwig-Maximilians-University, Munich, Germany.
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26
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Voigtlander R, Haase R, Mück-Hausl M, Zhang W, Boehme P, Lipps HJ, Schulz E, Baiker A, Ehrhardt A. A Novel Adenoviral Hybrid-vector System Carrying a Plasmid Replicon for Safe and Efficient Cell and Gene Therapeutic Applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2013; 2:e83. [PMID: 23549553 PMCID: PMC3650243 DOI: 10.1038/mtna.2013.11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In dividing cells, the two aims a gene therapeutic approach should accomplish are efficient nuclear delivery and retention of therapeutic DNA. For stable transgene expression, therapeutic DNA can either be maintained by somatic integration or episomal persistence of which the latter approach would diminish the risk of insertional mutagenesis. As most monosystems fail to fulfill both tasks with equal efficiency, hybrid-vector systems represent promising alternatives. Our hybrid-vector system synergizes high-capacity adenoviral vectors (HCAdV) for efficient delivery and the scaffold/matrix attachment region (S/MAR)–based pEPito plasmid replicon for episomal persistence. After proving that this plasmid replicon can be excised from adenovirus in vitro, colony forming assays were performed. We found an increased number of colonies of up to sevenfold in cells that received the functional plasmid replicon proving that the hybrid-vector system is functional. Transgene expression could be maintained for 6 weeks and the extrachromosomal plasmid replicon was rescued. To show efficacy in vivo, the adenoviral hybrid-vector system was injected into C57Bl/6 mice. We found that the plasmid replicon can be released from adenoviral DNA in murine liver resulting in long-term transgene expression. In conclusion, we demonstrate the efficacy of our novel HCAdV-pEPito hybrid-vector system in vitro and in vivo.
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Affiliation(s)
- Richard Voigtlander
- 1] Virology, Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Munich, Germany [2] Current address: Research Laboratory Endocrinology, University Hospital Essen, Essen, Germany
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27
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Koirala A, Makkia RS, Conley SM, Cooper MJ, Naash MI. S/MAR-containing DNA nanoparticles promote persistent RPE gene expression and improvement in RPE65-associated LCA. Hum Mol Genet 2013; 22:1632-42. [PMID: 23335596 DOI: 10.1093/hmg/ddt013] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations in genes in the retinal pigment epithelium (RPE) cause or contribute to debilitating ocular diseases, including Leber's congenital amaurosis (LCA). Genetic therapies, particularly adeno-associated viruses (AAVs), are a popular choice for monogenic diseases; however, the limited payload capacity of AAVs combined with the large number of retinal disease genes exceeding that capacity make the development of alternative delivery methods critical. Here, we test the ability of compacted DNA nanoparticles (NPs) containing a plasmid with a scaffold matrix attachment region (S/MAR) and vitelliform macular dystrophy 2 (VMD2) promoter to target the RPE, drive long-term, tissue-specific gene expression and mediate proof-of-principle rescue in the rpe65(-/-) model of LCA. We show that the S/MAR-containing plasmid exhibited reporter gene expression levels several fold higher than plasmid or NPs without S/MARs. Importantly, this expression was highly persistent, lasting up to 2 years (last timepoint studied). We therefore selected this plasmid for testing in the rpe65(-/-) mouse model and observe that NP or plasmid VMD2-hRPE65-S/MAR led to structural and functional improvements in the LCA disease phenotype. These results indicate that the non-viral delivery of hRPE65 vectors can result in persistent, therapeutically efficacious gene expression in the RPE.
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Affiliation(s)
- Adarsha Koirala
- Department of Cell Biology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, BMSB 781, Oklahoma City, OK 73104, USA
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Zhao Q, Lu B, George SK, Yoo JJ, Atala A. Safeguarding pluripotent stem cells for cell therapy with a non-viral, non-integrating episomal suicide construct. Biomaterials 2012; 33:7261-71. [DOI: 10.1016/j.biomaterials.2012.06.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/22/2012] [Indexed: 02/03/2023]
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Hagedorn C, Baiker A, Postberg J, Ehrhardt A, Lipps HJ. Handling S/MAR vectors. Cold Spring Harb Protoc 2012; 2012:657-63. [PMID: 22661441 DOI: 10.1101/pdb.top068262] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nonviral episomal vectors represent attractive alternatives to currently used virus-based expression systems. In the late 1990s, it was shown that a plasmid containing an expression cassette linked to a scaffold/matrix attached region (S/MAR) replicates as a low copy number episome in all cell lines tested, as well as primary cells, and can be used for the genetic modification of higher animals. Once established in the cell, the S/MAR vector replicates early during S-phase and, in the absence of selection, is stably retained in the cells for an unlimited period of time. This vector can therefore be regarded as a minimal model system for studying the epigenetic regulation of replication and functional nuclear architecture. In theory, this construct represents an almost "ideal" expression system for gene therapy. In practice, S/MAR-based vectors stably modify mammalian cells with efficiencies far below those of virus-based constructs. Consequently, they have not yet found application in gene therapy trials. Furthermore, S/MAR vector systems are not trivial to handle and several critical technical issues have to be considered when modifying these vectors for various applications.
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Affiliation(s)
- Claudia Hagedorn
- Centre for Biomedical Education and Research, Institute of Cell Biology, University of Witten/Herdecke, 58453 Witten, Germany
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Hsu CYM, Uludağ H. Nucleic-acid based gene therapeutics: delivery challenges and modular design of nonviral gene carriers and expression cassettes to overcome intracellular barriers for sustained targeted expression. J Drug Target 2012; 20:301-28. [PMID: 22303844 DOI: 10.3109/1061186x.2012.655247] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The delivery of nucleic acid molecules into cells to alter physiological functions at the genetic level is a powerful approach to treat a wide range of inherited and acquired disorders. Biocompatible materials such as cationic polymers, lipids, and peptides are being explored as safer alternatives to viral gene carriers. However, the comparatively low efficiency of nonviral carriers currently hampers their translation into clinical settings. Controlling the size and stability of carrier/nucleic acid complexes is one of the primary hurdles as the physicochemical properties of the complexes can define the uptake pathways, which dictate intracellular routing, endosomal processing, and nucleocytoplasmic transport. In addition to nuclear import, subnuclear trafficking, posttranscriptional events, and immune responses can further limit transfection efficiency. Chemical moieties, reactive linkers or signal peptide have been conjugated to carriers to prevent aggregation, induce membrane destabilization and localize to subcellular compartments. Genetic elements can be inserted into the expression cassette to facilitate nuclear targeting, delimit expression to targeted tissue, and modulate transgene expression. The modular option afforded by both gene carriers and expression cassettes provides a two-tier multicomponent delivery system that can be optimized for targeted gene delivery in a variety of settings.
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Affiliation(s)
- Charlie Yu Ming Hsu
- Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Cananda
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Hagedorn C, Wong SP, Harbottle R, Lipps HJ. Scaffold/Matrix Attached Region-Based Nonviral Episomal Vectors. Hum Gene Ther 2011; 22:915-23. [DOI: 10.1089/hum.2011.084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Claudia Hagedorn
- Centre for Biomedical Education and Research, Institute of Cell Biology, University Witten/Herdecke, 58453 Witten, Germany
| | - Suet-Ping Wong
- Gene Therapy Research Group, Section of Molecular Medicine, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Richard Harbottle
- Gene Therapy Research Group, Section of Molecular Medicine, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hans J. Lipps
- Centre for Biomedical Education and Research, Institute of Cell Biology, University Witten/Herdecke, 58453 Witten, Germany
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Argyros O, Wong SP, Harbottle RP. Non-viral episomal modification of cells using S/MAR elements. Expert Opin Biol Ther 2011; 11:1177-91. [PMID: 21548848 DOI: 10.1517/14712598.2011.582035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The early potential of gene therapy is slowly becoming realized following the recent treatment of patients with severe combined immunodeficiency and ocular diseases. However at present the field of gene therapy is tempered by the toxicity issues, mainly that of the integrated retroviral vector used in most trials which led to oncogenesis in several of the treated patients. The development of safer, alternative vectors is therefore vital for further progress in this field, in particular vectors which remain episomal and are therefore less genotoxic. One such unique class of vectors are those based on scaffold matrix attachment regions (S/MARs) elements, which are maintained extra-chromosomally and replicate in vitro and in vivo. AREAS COVERED The overview here describes the most relevant studies utilizing the S/MAR element to episomally modify mammalian cells and tissues with a particular focus on liver tissue, as well as the brain, the muscle, the eye, cancer cells, embryonic cells and neonatal mice. For this purpose, recently published data in these areas (mainly articles published between 2000 and 2010) are reviewed. EXPERT OPINION The utilisation of vectors harbouring an S/MAR element is an efficient, safe and cost-effective way to episomally modify mammalian cells.
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Affiliation(s)
- Orestis Argyros
- Imperial College London, Gene Therapy Research Group, Sir Alexander Fleming Building, National Heart and Lung Institute, South Kensington, London SW7 2AZ, UK.
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Wade-Martins R. Developing extrachromosomal gene expression vector technologies: an overview. Methods Mol Biol 2011; 738:1-17. [PMID: 21431716 DOI: 10.1007/978-1-61779-099-7_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Extrachromosomal, or episomal, vectors offer a number of advantages for therapeutic and scientific applications compared to integrating vectors. Extrachromosomal vectors persist in the nucleus without the requirement to integrate into the host genome, hence avoiding the recent concerns surrounding the genotoxic effects of vector integration. By avoiding integration, episomal vectors avoid vector rearrangement, which can occur at integration, and also avoid any effect of surrounding DNA activity on transgene expression ("position effect"). Extrachromosomal vectors offer a very high transgene capacity, allowing either the incorporation of large promoter and regulatory elements into an expression cassette, or the use of complete genomic loci of up to 100 kb or larger as transgenes. Whole genomic loci transgenes offer an elegant means to express genes under physiological and developmental-stage regulation, to express multiple transcript variants from a single locus, and to express multiple genes from a single tract of genomic DNA. The combined advantages of episomal vectors of prolonged transgene persistence in the absence of vector integration, avoiding silencing by flanking heterochromatin, and high capacity, facilitating delivery and expression of genomic DNA transgenes, will be reviewed here and potential therapeutic and scientific uses outlined.
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Affiliation(s)
- Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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Tessadori F, Zeng K, Manders E, Riool M, Jackson D, van Driel R. Stable S/MAR-based episomal vectors are regulated at the chromatin level. Chromosome Res 2010; 18:757-75. [PMID: 21080054 PMCID: PMC2996544 DOI: 10.1007/s10577-010-9165-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 10/23/2010] [Accepted: 10/25/2010] [Indexed: 02/02/2023]
Abstract
Episomal vectors assembled from defined genetic components are a promising alternative to traditional gene therapy vectors that integrate in the host genome and may cause insertional mutations. The vector pEPI-eGFP is stably retained in the episomal state in cultured mammalian cells at low copy number for many generations without integration into the host genome. Although pEPI-eGFP is a fully engineered vector, little is known about how it interacts with the host genome and about the molecular mechanisms that are responsible for its transcriptional activity. We have analyzed the expression of the episomal reporter gene eGFP under conditions that affect the chromatin state of the genome. We have also constructed pEPI derivatives carrying a tandem array of lac operator sequences, which allows in vivo visualization and manipulation of the chromatin state of the episome. We show that changes in chromatin state of both the host and pEPI-eGFP induces changes in episomal gene activity and influences the episome’s nuclear distributions. We conclude that episomal genes are subject to control systems of the host, similarly to their counterparts in the host genome.
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Affiliation(s)
- Federico Tessadori
- Swammerdam Institute for Life Sciences, University of Amsterdam, P.O. Box 94215, 1090GE, Amsterdam, The Netherlands.
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Rupprecht S, Hagedorn C, Seruggia D, Magnusson T, Wagner E, Ogris M, Lipps HJ. Controlled removal of a nonviral episomal vector from transfected cells. Gene 2010; 466:36-42. [PMID: 20621169 DOI: 10.1016/j.gene.2010.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 06/22/2010] [Accepted: 07/01/2010] [Indexed: 10/19/2022]
Abstract
An ideal vector to be used in gene therapy should allow long-term and regulated expression of the therapeutic sequence, but in many cases, it would be most desirable to remove all ectopic vector sequences from the cell once expression is no longer required. The vector pEPI is the first nonviral autonomous replicon that was constructed for mammalian cells. It represents a minimal model system to study the epigenetic regulation of replication and transcription but is also regarded as a promising alternative to currently used viral vector systems in gene therapy. Its function relies on a transcription unit linked to an S/MAR sequence. We constructed an inducible pEPI vector system based on the Tet ON system in which transcription is switched on in the presence of doxycycline. We show that for vector replication and long-term maintenance an ongoing transcription running into the S/MAR element is required. Once established, the vector is lost from the cell upon switching off transcription from the gene linked to the S/MAR. This feature provides not only controlled transgene expression but also the possibility to remove all vector molecules from the cells upon demand. This inducible episomal nonviral vector system will find broad application in gene therapy but also in reprogramming of somatic cells or modification of stem cells.
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Affiliation(s)
- Sina Rupprecht
- Institute of Cell Biology, ZBAF, University Witten/Herdecke, Witten, Germany
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36
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Haase R, Argyros O, Wong SP, Harbottle RP, Lipps HJ, Ogris M, Magnusson T, Vizoso Pinto MG, Haas J, Baiker A. pEPito: a significantly improved non-viral episomal expression vector for mammalian cells. BMC Biotechnol 2010; 10:20. [PMID: 20230618 PMCID: PMC2847955 DOI: 10.1186/1472-6750-10-20] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 03/15/2010] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The episomal replication of the prototype vector pEPI-1 depends on a transcription unit starting from the constitutively expressed Cytomegalovirus immediate early promoter (CMV-IEP) and directed into a 2000 bp long matrix attachment region sequence (MARS) derived from the human beta-interferon gene. The original pEPI-1 vector contains two mammalian transcription units and a total of 305 CpG islands, which are located predominantly within the vector elements necessary for bacterial propagation and known to be counterproductive for persistent long-term transgene expression. RESULTS Here, we report the development of a novel vector pEPito, which is derived from the pEPI-1 plasmid replicon but has considerably improved efficacy both in vitro and in vivo. The pEPito vector is significantly reduced in size, contains only one transcription unit and 60% less CpG motives in comparison to pEPI-1. It exhibits major advantages compared to the original pEPI-1 plasmid, including higher transgene expression levels and increased colony-forming efficiencies in vitro, as well as more persistent transgene expression profiles in vivo. The performance of pEPito-based vectors was further improved by replacing the CMV-IEP with the human CMV enhancer/human elongation factor 1 alpha promoter (hCMV/EF1P) element that is known to be less affected by epigenetic silencing events. CONCLUSIONS The novel vector pEPito can be considered suitable as an improved vector for biotechnological applications in vitro and for non-viral gene delivery in vivo.
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Affiliation(s)
- Rudolf Haase
- Max von Pettenkofer-Institute, University of Munich, Munich, Germany
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Broll S, Oumard A, Hahn K, Schambach A, Bode J. Minicircle performance depending on S/MAR-nuclear matrix interactions. J Mol Biol 2009; 395:950-65. [PMID: 20004666 DOI: 10.1016/j.jmb.2009.11.066] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/14/2009] [Accepted: 11/30/2009] [Indexed: 12/12/2022]
Abstract
The ideal vector for cell and tissue modification does not depend on integration but rather behaves as an independent functional unit that replicates as an episome. Based on a scaffold/matrix attachment region (S/MAR), we have introduced, in 2006, an approximately 4-kb replicating nonviral minicircle able to exploit the cellular replication machinery in a way reminiscent of ARS vectors. Consisting of only one active transcription unit and the S/MAR, it resists silencing as it is free of prokaryotic vector parts and drug selection markers. The rate of final establishment in the nuclear architecture is moderate but comparable to Epstein-Barr virus-based episomes (<5%). Here, we demonstrate that this parameter can be improved if the host cell chromatin is opened by histone hyperacetylation prior to transfection. It remains unaffected, however, by cell cycle position. Still, this class of episomes revealed intrinsic instability and integration after 5 months of continuous culture. In vivo evolution enabled the effective reduction of S/MAR size from 2 kb to 733 bp (resulting in a minicircle of approximately 3 kb) with largely improved stability and cloning capacity. Investigation of individual clones served to prove persistent and homogenous expression, which is ascribed to stable association with nuclear attachment sites. Optimum expression levels were shown to depend on the authentic usage of a polyadenylation site 3' from the S/MAR as anticipated by the stress-induced duplex destabilization algorithm, which finds increasing use to predict the functional parameters of these systems.
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Affiliation(s)
- Sandra Broll
- Department Molecular Biotechnology/Epigenetic Regulation, Helmholtz Center for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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Sgourou A, Routledge S, Spathas D, Athanassiadou A, Antoniou MN. Physiological levels of HBB transgene expression from S/MAR element-based replicating episomal vectors. J Biotechnol 2009; 143:85-94. [DOI: 10.1016/j.jbiotec.2009.06.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 03/22/2009] [Accepted: 06/16/2009] [Indexed: 01/29/2023]
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Rupprecht S, Lipps HJ. Cell cycle dependent histone dynamics of an episomal non-viral vector. Gene 2009; 439:95-101. [PMID: 19306916 DOI: 10.1016/j.gene.2009.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 03/11/2009] [Accepted: 03/12/2009] [Indexed: 01/12/2023]
Abstract
Non-viral episomal vectors are regarded as attractive alternatives to currently used virus-based vectors in gene therapy. In addition, they represent a minimal model system to study the epigenetic control of basic nuclear processes, such as transcription, replication and nuclear retention. Here we analyze the dynamics of histone modifications during the cell cycle of the episomally replicating vector pEPI-eGFP. The histone code of pEPI-eGFP was compared to its integrating counterpart pGFP-C1. We found that pEPI-eGFP is preferentially associated with histone modifications typical for active chromatin, while pGFP-C1 is mostly decorated with repressive histone modifications. During interphase the distribution of histone modification on pEPI-eGFP is very non-dynamic; the S/MAR shows the highest concentration of active histone modifications. However, they are specifically removed during mitosis and this may correlate with the association and co-segregation of pEPI with the host chromosomes during cell division.
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Affiliation(s)
- Sina Rupprecht
- Institute of Cell Biology, University Witten/Herdecke, Stockumer Str. 10, D 58453 Witten, FRG
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40
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Giannakopoulos A, Stavrou EF, Zarkadis I, Zoumbos N, Thrasher AJ, Athanassiadou A. The functional role of S/MARs in episomal vectors as defined by the stress-induced destabilization profile of the vector sequences. J Mol Biol 2009; 387:1239-49. [PMID: 19248788 DOI: 10.1016/j.jmb.2009.02.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 02/06/2009] [Accepted: 02/12/2009] [Indexed: 11/28/2022]
Abstract
The scaffold/matrix attachment regions (S/MARs) are chromosomal elements that participate in the formation of chromatin domains and have origin of replication support functions. Because of all these functions, in recent years, they have been used as part of episomal vectors for gene transfer. The S/MAR of the human beta-interferon gene has been shown to support efficient episome retention and transgene expression in various mammalian cells. In Jurkat and other cells, DNA plasmid vectors containing Epstein-Barr virus origin of replication (EBV OriP) and the EBV nuclear antigen-1 gene mediate prolonged episome retention in the host cell nucleus, which, however, diminishes over time. In order to enhance retention, we combined this system with an S/MAR element. Unexpectedly, this completely eliminated the capacity of episomes to replicate. Calculation of the stress-induced DNA duplex destabilization profile of the vectors suggested that the S/MAR element had created an increase in molecular stability at the OriP site that may have disturbed replicative potential. In contrast, introduction of an alternative initiation of replication region from the beta-globin gene locus, instead of EBV OriP and the EBV nuclear antigen-1 gene, restored replicative capacity and enhanced episome retention mediated by the S/MAR. These effects were associated with a destabilization profile at the initiation of replication region. These data demonstrate a correlation between S/MAR-mediated vector retention and the presence of an unstable duplex at a replication origin, in this particular setting. We consider that the calculation of stress-induced duplex destabilization may be an informative first step in the design of units that replicate extrachromosomally, particularly as the latter present a safer and, therefore, attractive alternative to integrating viral vectors for gene therapy applications.
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Abstract
Regulatory mechanisms for DNA replication are crucial to the control of the cell cycle in eukaryotic cells. One of the widely used assays to understand the complex mammalian replication system is the cell-free in vitro replication assay (IVRA). IVRA can provide a snapshot of the regulatory mechanisms controlling replication in higher eukaryotes by using a single plasmid, pEPI-1. This chapter outlines the general strategies and protocols used to perform IVRA to study the differential recruitment of replication factors either independently or in combination, based on the experience in studying the role of prohibitin in replication as well as other published protocols. This method can be employed to identify not only proteins that assist replication but also proteins that inhibit replication of mammalian genome.
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Affiliation(s)
- Wasia Rizwani
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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42
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Argyros O, Wong SP, Niceta M, Waddington SN, Howe SJ, Coutelle C, Miller AD, Harbottle RP. Persistent episomal transgene expression in liver following delivery of a scaffold/matrix attachment region containing non-viral vector. Gene Ther 2008; 15:1593-605. [PMID: 18633447 DOI: 10.1038/gt.2008.113] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An ideal gene therapy vector should enable persistent transgene expression without limitations of safety and reproducibility. Here we report the development of a non-viral episomal plasmid DNA (pDNA) vector that appears to fulfil these criteria. This pDNA vector combines a scaffold/matrix attachment region (S/MAR) with a human liver-specific promoter (alpha1-antitrypsin (AAT)) in such a way that long-term expression is enabled in murine liver following hydrodynamic injection. Long-term expression is demonstrated by monitoring the longitudinal luciferase expression profile for up to 6 months by means of in situ bioluminescent imaging. All relevant control pDNA constructs expressing luciferase are unable to sustain significant transgene expression beyond 1 week post-administration. We establish that this shutdown of expression is due to promoter methylation. In contrast, the S/MAR element appears to inhibit methylation of the AAT promoter thereby preventing transgene silencing. Although this vector appears to be maintained as an episome throughout, we have no evidence for its establishment as a replicating entity. We conclude that the combination of a mammalian, tissue-specific promoter with the S/MAR element is sufficient to drive long-term episomal pDNA expression of genes in vivo.
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Affiliation(s)
- O Argyros
- Department of Chemistry, Imperial College Genetic Therapies Centre, Imperial College London, London, UK
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43
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Lufino MMP, Edser PAH, Wade-Martins R. Advances in high-capacity extrachromosomal vector technology: episomal maintenance, vector delivery, and transgene expression. Mol Ther 2008; 16:1525-38. [PMID: 18628754 DOI: 10.1038/mt.2008.156] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Recent developments in extrachromosomal vector technology have offered new ways of designing safer, physiologically regulated vectors for gene therapy. Extrachromosomal, or episomal, persistence in the nucleus of transduced cells offers a safer alternative to integrating vectors which have become the subject of safety concerns following serious adverse events in recent clinical trials. Extrachromosomal vectors do not cause physical disruption in the host genome, making these vectors safe and suitable tools for several gene therapy targets, including stem cells. Moreover, the high insert capacity of extrachromosomal vectors allows expression of a therapeutic transgene from the context of its genomic DNA sequence, providing an elegant way to express normal splice variants and achieve physiologically regulated levels of expression. Here, we describe past and recent advances in the development of several different extrachromosomal systems, discuss their retention mechanisms, and evaluate their use as expression vectors to deliver and express genomic DNA loci. We also discuss a variety of delivery systems, viral and nonviral, which have been used to deliver episomal vectors to target cells in vitro and in vivo. Finally, we explore the potential for the delivery and expression of extrachromosomal transgenes in stem cells. The long-term persistence of extrachromosomal vectors combined with the potential for stem cell proliferation and differentiation into a wide range of cell types offers an exciting prospect for therapeutic interventions.
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Affiliation(s)
- Michele M P Lufino
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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Long-term suppression of hepatitis B virus replication by short hairpin RNA expression using the scaffold/matrix attachment region-based replicating vector system pEPI-1. Antimicrob Agents Chemother 2008; 52:2355-9. [PMID: 18474581 DOI: 10.1128/aac.00067-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Since the emergence of viral resistance of hepatitis B virus (HBV) during treatment is becoming an important issue even with newer drugs, there is a need for alternative treatment options such as, for example, RNA interference (RNAi) technology. While short-term suppression of HBV replication is easily achieved with small interfering RNA oligonucleotides, this is not the case for long-term suppression due to the lack of an optimal vector system. Based on the nonviral scaffold/matrix attachment region (S/MAR)-based vector system pEPI-1, which is free of common side effects and is stably retained as an episome even in the absence of selection, we designed a short hairpin RNA (shRNA) expression vector called pEPI-RNAi for HBV suppression. HBV-replicating HepG2.2.15 cells were transfected with pEPI-RNAi, and the intracellular status of the plasmid was followed by PCR and Southern analysis. HBV replication was measured on the DNA, RNA, and protein level. HBV RNA expression was reduced by almost 85% 3 months posttransfection with pEPI-RNAi. At 8 months posttransfection in the absence of antibiotic selection pressure, the suppression level was still 70% and the vector was retained as an episome. The reduction of total intracellular HBV DNA at this point was 77%, showing a marked suppression of HBV DNA replication. At a comparable level, secretion of viral antigens, as well as progeny HBV virions, was inhibited. The S/MAR-based vector system pEPI-1 allows long-term suppression of HBV replication by the expression of suitable shRNAs. Due to its unique properties compared to commonly used vectors, it provides an interesting option for the treatment of chronically HBV-infected individuals.
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Direct comparison of hepatocyte-specific expression cassettes following adenoviral and nonviral hydrodynamic gene transfer. Gene Ther 2008; 15:594-603. [PMID: 18288213 DOI: 10.1038/sj.gt.3303096] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hepatocytes are a key target for treatment of inborn errors of metabolism, dyslipidemia and coagulation disorders. The development of potent expression cassettes is a critical target to improve the therapeutic index of gene transfer vectors. Here we evaluated 22 hepatocyte-specific expression cassettes containing a human apo A-I transgene following hydrodynamic transfer of plasmids or adenoviral transfer with E1E3E4-deleted vectors in C57BL/6 mice. The DC172 promoter consisting of a 890 bp human alpha(1)-antitrypsin promoter and two copies of the 160 bp alpha(1)-microglobulin enhancer results in superior expression levels compared to constructs containing the 1.5 kb human alpha(1)-antitrypsin promoter, the 790 bp synthetic liver-specific promoter or the DC190 promoter containing a 520 bp human albumin promoter and two copies of the 99 bp prothrombin enhancer. The most potent expression cassette consists of the DC172 promoter upstream of the transgene and two copies of the hepatic control region-1. Minicircles containing this expression cassette induce persistent physiological human apo A-I or human factor IX levels after hydrodynamic transfer. In conclusion, in this comparative study of 22 hepatocyte-specific expression cassettes, the DC172 promoter in combination with two copies of the hepatic control region-1 induces the highest expression levels following hydrodynamic and adenoviral transfer.
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Hashizume T, Shimizu N. Dissection of mammalian replicators by a novel plasmid stability assay. J Cell Biochem 2007; 101:552-65. [PMID: 17226771 DOI: 10.1002/jcb.21210] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A plasmid, bearing a mammalian replication initiation region (IR) and a matrix attachment region (MAR) was previously shown to be efficiently amplified to high copy number in mammalian cells and to generate chromosomal homogeneously staining regions (HSRs). The amplification mechanism was suggested to entail a head-on collision at the MAR between the transcription machinery and the hypothetical replication fork arriving from the IR, leading to double strand breakage (DSB) that triggered HSR formation. The experiments described here show that such plasmids are stabilized if collisions involving not only promoter-driven transcription but also promoter-independent transcription are avoided, and stable plasmids appeared to persist as submicroscopic episomes. These findings suggest that the IR sequence that promotes HSR generation may correspond to the sequence that supports replication initiation (replicator). Thus, we developed a "plasmid stability assay" that sensitively detects the activity of HSR generation in a test sequence. The assay was used to dissect two replicator regions, derived from the c-myc and DHFR ori-beta loci. Consequently, minimum sequences that efficiently promoted HSR generation were identified. They included several sequence elements, most of which coincided with reported replicator elements. These data and this assay will benefit studies of replication initiation and applications that depend on plasmid amplification.
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Affiliation(s)
- Toshihiko Hashizume
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8521, Japan
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Establishment and mitotic stability of an extra-chromosomal mammalian replicon. BMC Cell Biol 2007; 8:33. [PMID: 17683605 PMCID: PMC1959191 DOI: 10.1186/1471-2121-8-33] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 08/06/2007] [Indexed: 11/15/2022] Open
Abstract
Background Basic functions of the eukaryotic nucleus, like transcription and replication, are regulated in a hierarchic fashion. It is assumed that epigenetic factors influence the efficiency and precision of these processes. In order to uncouple local and long-range epigenetic features we used an extra-chromosomal replicon to study the requirements for replication and segregation and compared its behavior to that of its integrated counterpart. Results The autonomous replicon replicates in all eukaryotic cells and is stably maintained in the absence of selection but, as other extra-chromosomal replicons, its establishment is very inefficient. We now show that following establishment the vector is stably associated with nuclear compartments involved in gene expression and chromosomal domains that replicate at the onset of S-phase. While the vector stays autonomous, its association with these compartments ensures the efficiency of replication and mitotic segregation in proliferating cells. Conclusion Using this novel minimal model system we demonstrate that relevant functions of the eukaryotic nucleus are strongly influenced by higher nuclear architecture. Furthermore our findings have relevance for the rational design of episomal vectors to be used for genetic modification of cells: in order to improve such constructs with respect to efficiency elements have to be identified which ensure that such constructs reach regions of the nucleus favorable for replication and transcription.
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Manzini S, Vargiolu A, Stehle IM, Bacci ML, Cerrito MG, Giovannoni R, Zannoni A, Bianco MR, Forni M, Donini P, Papa M, Lipps HJ, Lavitrano M. Genetically modified pigs produced with a nonviral episomal vector. Proc Natl Acad Sci U S A 2006; 103:17672-7. [PMID: 17101993 PMCID: PMC1635978 DOI: 10.1073/pnas.0604938103] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Genetic modification of cells and animals is an invaluable tool for biotechnology and biomedicine. Currently, integrating vectors are used for this purpose. These vectors, however, may lead to insertional mutagenesis and variable transgene expression and can undergo silencing. Scaffold/matrix attachment region-based vectors are nonviral expression systems that replicate autonomously in mammalian cells, thereby making possible safe and reliable genetic modification of higher eukaryotic cells and organisms. In this study, genetically modified pig fetuses were produced with the scaffold/matrix attachment region-based vector pEPI, delivered to embryos by the sperm-mediated gene transfer method. The pEPI vector was detected in 12 of 18 fetuses in the different tissues analyzed and was shown to be retained as an episome. The reporter gene encoded by the pEPI vector was expressed in 9 of 12 genetically modified fetuses. In positive animals, all tissues analyzed expressed the reporter gene; moreover in these tissues, the positive cells were on the average 79%. The high percentage of EGFP-expressing cells and the absence of mosaicism have important implications for biotechnological and biomedical applications. These results are an important step forward in animal transgenesis and can provide the basis for the future development of germ-line gene therapy.
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Affiliation(s)
- Stefano Manzini
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
| | - Alessia Vargiolu
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
| | - Isa M Stehle
- Institute of Cell Biology, Witten/Herdecke University, 58448 Witten, Germany
| | - Maria Laura Bacci
- Department of Veterinary Morphophysiology and Animal Production, University of Bologna, 40064 Bologna, Italy
| | - Maria Grazia Cerrito
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
| | - Roberto Giovannoni
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
| | - Augusta Zannoni
- Department of Veterinary Morphophysiology and Animal Production, University of Bologna, 40064 Bologna, Italy
| | - Maria Rosaria Bianco
- Centro Regionale di Competenza Applicazioni Tecnologico-Industriali di Biomolecole e Biosistemi-BioTekNet-Seconda Università di Napoli, 80138 Naples, Italy; and
| | - Monica Forni
- Department of Veterinary Morphophysiology and Animal Production, University of Bologna, 40064 Bologna, Italy
| | - Pierluigi Donini
- Department of Cellular and Developmental Biology, La Sapienza University, 00185 Rome, Italy
| | - Michele Papa
- Centro Regionale di Competenza Applicazioni Tecnologico-Industriali di Biomolecole e Biosistemi-BioTekNet-Seconda Università di Napoli, 80138 Naples, Italy; and
| | - Hans J Lipps
- Institute of Cell Biology, Witten/Herdecke University, 58448 Witten, Germany
| | - Marialuisa Lavitrano
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
- To whom correspondence should be addressed. E-mail:
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Wang Y, Tang Q, Maul GG, Yuan Y. Kaposi's sarcoma-associated herpesvirus ori-Lyt-dependent DNA replication: dual role of replication and transcription activator. J Virol 2006; 80:12171-86. [PMID: 17020951 PMCID: PMC1676287 DOI: 10.1128/jvi.00990-06] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lytic replication of Kaposi's sarcoma-associated herpesvirus (KSHV) is essential for viral propagation and pathogenicity. In Kaposi's sarcoma lesions, constant lytic replication plays a role in sustaining the population of latently infected cells that otherwise are quickly lost by segregation of latent viral episomes as spindle cells divide. Lytic DNA replication initiates from an origin (ori-Lyt) and requires trans-acting elements. Two functional ori-Lyts have been identified in the KSHV genome. Some cis-acting and trans-acting elements for ori-Lyt-dependent DNA replication have been found. Among these, K8 binding sites, a cluster of C/EBP binding motifs, and a replication and transcription activator (RTA) responsive element (RRE) are crucial cis-acting elements. Binding of K8 and RTA proteins to these motifs in ori-Lyt DNA was demonstrated to be absolutely essential for DNA replication. In the present study, functional roles of RTA in ori-Lyt-dependent DNA replication have been investigated. Two distinct functions of RTA were revealed. First, RTA activates an ori-Lyt promoter and initiates transcription across GC-rich tandem repeats. This RTA-mediated transcription is indispensable for DNA replication. Second, RTA is a component of the replication compartment, where RTA interacts with prereplication complexes composed of at least six core machinery proteins and K8. The prereplication complexes are recruited to ori-Lyt DNA through RTA, which interacts with the RRE, as well as K8, which binds to a cluster of C/EBP binding motifs with the aid of C/EBP alpha. The revelation of these two functions of RTA, together with its role in initiation of a transcriptional cascade that leads to transcription of all viral lytic genes, shows that RTA is a critical initiator and regulator of KSHV lytic DNA replication and viral propagation.
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Affiliation(s)
- Yan Wang
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th Street, Philadelphia, PA 19104, USA
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Jackson DA, Juranek S, Lipps HJ. Designing nonviral vectors for efficient gene transfer and long-term gene expression. Mol Ther 2006; 14:613-26. [PMID: 16784894 DOI: 10.1016/j.ymthe.2006.03.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 03/20/2006] [Accepted: 03/20/2006] [Indexed: 01/20/2023] Open
Abstract
Although the genetic therapy of human diseases has been conceptually possible for many years we still lack a vector system that allows safe and reproducible genetic modification of eukaryotic cells and ensures faithful long-term expression of transgenes. There is increasing agreement that vectors that are based exclusively on chromosomal elements, which replicate autonomously in human cells, could fulfill these criteria. The rational construction of such vectors is still hindered by our limited knowledge of the factors that regulate chromatin function in eukaryotic cells. This review sets out to summarize how our current knowledge of nuclear organization can be applied to the design of extrachromosomal gene expression vectors that can be used for human gene therapy. Within the past years a number of episomal nonviral constructs have been designed and their replication strategies, expression of transgenes, mitotic stability, and delivery strategies and the mechanisms required for their stable establishment will be discussed. To date, these nonviral vectors have not been used in clinical trials. Even so, many compelling arguments can be developed to support the view that nonviral vector systems will play a major role in future gene therapy protocols.
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Affiliation(s)
- Dean A Jackson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
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